As The War Rages (A Phantom Menace re-write)
by Joeneauxvieve
Summary: Basically how I think the prequels should have gone. (discontinued until further notice)
1. Prologue

Prologue

Gunshots and blaster bolts tumbled through the air and it stayed that way. This war which has unknown motives quickly escalated. Now it was one of the largest galactic wars known to anybody. Not even Master Yoda, who has been alive for nearly a millennia, has witnessed anything so devastating. This was a time of a galaxy divided. Republic forces, along with all the Jedi they could muster, have done their best to protect numerous galactic systems from this unknown enemy, and the mysterious army of clone troopers; the origins unknown. As the Jedi are spread thinly across the galaxy, this has left more and more opportunity for the mysterious opponent to strike. Not even the most powerful of these Force-sensitive knights have not been successful in tracking down the enemy; only receiving fragments of battle strategies thus far. There are theories of who this person or these people might be; which has led some to break from the Republic to form their own militia and their own allies.

Tatooine was the next targeted planet in this galactic devastation. Fortunately, the enemy has invaded the planet after whispers of it reached the ears of the Jedi counsel. By the time it did, There was still time for a planetary rescue, but it would be days before they could help survivors if there were any. Proper medical care, food, water along with many other necessities were required before they could even consider looking for them.

Meanwhile on Tatooine, Shmi Skywalker and disgraced Jedi knight Greng Kosh were hiding in their home attempting to wait out the battle and protect their young son, Anakin Skywalker. However, this proved to be more and more of a struggle for the family as the clone army advanced nearer and nearer while the invasion progressed.

"I must go," said Greng. "I may not be able to stop them, but I can definitely slow them down."

"No, Greng, please. What about our son?" Shmi replied, implying her fear of her husband's death.

"Shmi, this the only way to keep Anakin alive. At least until the other Jedi come to scope the planet for survivors."

"But he needs you… He loves you."

Greng didn't pay attention the last comment. Anakin turned his gaze to where his parents were talking from the corner he sat in. Greng faced his son and told him "you have a powerful gift, son. You can use it in many ways. Use it for the right reasons," Anakin was confused as to what his father meant, but was instantly distracted as he took notice of his father grabbing a misshapen cylinder from his belt and watched him walk out of the homestead into the night. Anakin heard a faint humming and saw a flash of green light following his father's exit.

Little did Anakin know that he would never see his father again.

His mother could hear the uniform footsteps of the clone troopers in the distance signifying that they were almost among them. Shmi stood up, lifted one of the floor mats and removed a large, heavy clay trapdoor. She ordered Anakin to keep silent and stay inside until help arrived, but neither of them knew when that was going to be. Anakin obliged and hid. Shmi replaced the trapdoor and rug just moments before the clones barged into the home.

"We have you surrounded," came a monotone voice from one of the clones. "Surrender or die."

"I'll never surrender to you mindless drones, or your cowardly leader," Shmi argued.

"This is your last chance to spare your life! We order you to surrender!" came the exact same voice from another soldier

"NO!"

That one clone ended her life that night. All Anakin could hear was the brief conversation between his mother and the clone troopers, the blaster bolt that was shot through her heart and then nothing. Anakin knew exactly what happened to her. As much as he didn't want to, he knew. He didn't dare go up. He silently cried himself to sleep in the dark and dusty basement.

The following day Anakin awoke to hear his door opening and the sound of faint footsteps. He pressed his ear to the trapdoor in attempt to interpret what was being happening.

Master Qui-Gon Jinn and padawan Obi-Wan Kenobi were undercover Jedi sent to investigate for any survivors on Tatooine from the invasion prior. The Republic sent out as many Jedi as they could. Although Tatooine wasn't very populated, it was still an incredibly large planet.

"Master, look," said Obi-Wan pointing to Shmi's corpse.

"The clones were definitely here," Qui-Gon finished, eyeing her. "Is there anyone else here?"

"I sense another presence, but I'm not sure from where," Obi-Wan answered.

Anakin couldn't take it anymore. The basement was dark and dusty and his curiosity forced him to see what was going on. He was still scared to go up, but he used his courage. He attempted to lift the trapdoor but he didn't have the muscle capacity. This caused Obi-Wan to take notice of the movement under one of the floor mats. Anakin struggled to lift the it. Obi-Wan rushed over and exposed and removed the dense clay slab. Both he and Qui-gon were stunned to see a 9-year-old boy Anakin climb out of the cellar and at the fact he survived a planetary invasion. Anakin slowly stood up, but he was still scared. He didn't know they were Jedi, and neither of his parents told him who or what exactly the _help_ was going to be.

"Hello," said Qui-Gon calmly. "My name is Qui-Gon Jinn. This is Obi-Wan Kenobi. We have come to bring survivors to safety. Can you tell us what your name is?"

"How do I know you're not lying?" Anakin asked, still frightened and extremely cautious. Obi-Wan glanced at the Jedi master. Qui-Gon replied with an implying nod.

"He and I are members of the Jedi Order. If you come with us you'll be safe."

"How do I know you're not lying?!" Anakin said again on the brink of tears.

"Anakin, what are your instincts telling you? Are we lying?" asked Qui-Gon.

"No… you're not. How do I know that?"

"For the exact same reason we know who you are and what you're capable of." Obi-Wan lifted the clay slab with help from the Force and slowly brought his hand into a fist causing the clay to gradually crumble under the pressure until is was no more than a pile of rubble. "Do you trust us now?"

"Y-Yes… I do," Anakin stuttered in shock.

"We can help you, Anakin. Come with us and we will show you the ways of the Force," said Obi-Wan.

"You're Jedi?" Anakin asked _Is this the gift Father said I have? The Force?_ He thought to himself.

"Yes, and we will be leaving soon, so I suggest you bring only what you need," said Qui-Gon. Anakin said nothing and ran into the next room.

"We must report this to the counsel, Master. They will know what to do with the boy."

"We will report to the counsel, young padawan. But I already know what to do with him."

"You do?"

"Your training is almost complete, Obi-Wan. It is time for you take the largest leap in your training. You will train this boy, teach him in the ways of the Force. The Force is your guide now, and this boy shall guide you as well; as you have with Yoda, believe it or not. He knows your ready. He is the wisest Jedi in the order." explained Qui-Gon.

"Are you certain I'm ready for such a great responsibility? Master Yoda said this himself?"

"This is what every Jedi trains for; to train the next generation of peace-keepers. Trust me, Obi-Wan, I know you. You're ready."

"Thank you, Master Qui-Gon. It has been an honor serving alongside you in this war as a padawan. I hope I will serve alongside you as a knight as well." Qui-Gon smiled in reply.

Anakin re-entered the room with a large back pack filled with clothes, rations, and a holophoto of him and his parents. Although he had no clue what to expect he was excited to find out. He still carried thoughts of his mother and father with him always. He promised himself to never forget them. Anakin took one final glance at his mother's lifeless body on the floor. Then turned around and walked away. He began crying and walked away from his home. He knew he would never go back to it. Anakin was devastated. He wanted this war to end. He vowed to become the most powerful Force-user someday and end it himself. This was his reason.


	2. The Assignment

Anakin multiplied his Force abilities swifter than any known Jedi in 1,000 years. He wielded his lightsaber so competently that when he was deflecting the blaster bolts, the blade remained a blue blur. He was almost evenly matched against Obi-Wan and won every duel with all young Jedi. He was a great mentor towards the younglings, and even showed them how to construct their own lightsabers. They all looked up to him. Each one hoping to be his student someday.

The Jedi counsel was very impressed with Anakin. They would supervise him in his training sessions in the temple with multiple floating orbs that intended to shoot him. It would always end the same way. The saber would always pierce through the center and everyone would watch as it eventually melted off of the energy blade. Even on the highest difficulty level, Anakin would always defeat them.

Obi-Wan interrupted one of his practices with urgent news. "Anakin, a word?" he asked.

Anakin pushed a button a remote on his wrist. Several mouse droids entered the room and swept away what was left of the partially melted and singed training orbs. He then went outside to meet his master in the courtyard.

"You summoned me, master?" Anakin replied professionally.

"Precisely," replied his master. "I have an important message and assignment."

"Good or bad news?" Anakin asked with less spirit.

"That depends on your view of the situation." said Obi-Wan. Anakin gave a slightly confused expression. "The senate felt it would be best if the Republic had an army of their own. An army to help damaged planets, and to hopefully prevent future invasion and destruction." Obi-wan paused, clearly thinking.

"Yes?" Anakin broke the silence.

"Let's walk."

Both master and student leave the courtyard and into the main building. Obi-Wan told Anakin how it has been voted by the senate to form a militia and they thought it would be best if the Jedi supervised and trained the soldiers. And the counsel agreed.

"That's a great idea!" Said Anakin after Obi-Wan finished.

"Personally, I am not very fond of the proposal. However, I am not on the counsel, therefore it is not my decision. But I admit, it would be beneficial to have reinforcements when fending of an invasion. But there is some crucial information and necessities required before carrying out this plan."

"Like what?"

"Bases, funding, ships, fighters, people willing to fight. Perhaps even a super weapon is times become desperate enough."

"Yes, but we have been dodging attacks, and chasing after this... shadow army for nearly ten years! They are always several steps ahead of us, and always seem to know our next move. So how are we supposed to win?" Anakin said with some frustration and anger in his tone.

Obi-Wan stopped at the door of a dark room. He pushed a glowing button on a control panel next to it. With a soft whirring, the doors separated leaving a diamond-shaped opening for them to walk through. Obi-wan removed a small computer chip from his pocket. When he installed it, instantly charted territories of the outer rim of the galaxy was projected as a fuzzy, light-blue hologram. On the projection was a white dot marking the most recently targeted planet. Geonosis.

"As you know, the... shadow army as you called it, most recently targeted this planet." Obi-Wan gestured to the holographic model of Geonosis. "Before the clones departed the planet, one of our allies placed a tracking beacon-"

"Oh, yeah? Their ships can detect and deactivate tracking beacons on the hulls of their ships in ten seconds flat. It's pointless," interrupted Anakin.

"Yes, I am aware. However, luck was on our side during that battle. It wasn't on the ship, it was on the armor of one of the clones." Obi-Wan resumed. "It was found, yes, but not before they came out of hyper space in this star system." The star system Obi-Wan was referring to highlighted itself by turning into a burgundy red.

"Did you locate the planet they stopped at?" Anakin asked.

"Not an official destination, no. But judging on their route it is most likely Kamino." The model holographic Kamino also turned a burgundy red.

"Wait, why are you telling me all of this?" Said Anakin.

"This is your assignment. Kamino is beyond Separatist space, the counsel wants you to infiltrate the base, and get as much intel as you can about our enemy."

"What kind of intel?"

"Anything you can manage. Just don't get caught." Obi-Wan said with a slightly dark tone in his voice.

Anakin was caught a little off guard with his reply. "Ok. When do I leave?"

"You will board a passenger ship to neutral space. There's one leaving for Mandalor in a half hour at docking bay 1218. From there you will board a cargo vessel. One of our spies is a co-pilot, she will be expecting you, and your disguise will be hidden aboard." Anakin stood by mentally noting his directions.

"What of the intel? Will I have anything to store it with?"

"Here." Obi-Wan handed him a multi-purpose data chip. "This should upload as much information in the time you give it." Anakin took the chip and placed it in a deep pocket. "We will communicate with this." He handed Anakin a transparent earpiece with an invisible wire and a clip on microphone on the end. "I understand, Master." Anakin said moments before he turned away.

Anakin headed for docking bay 1218. As he walked he put the earpiece on and hid the microphone in his robes. When he arrived to depot of ships with many people loading and unloading the luggage and other passengers. Anakin stopped and observed the deck.

"Anakin? Can you hear me?" He heard Obi-Wan over the tiny speaker.

"Loud and clear, Master." Anakin replied.

"The freighter you are to board is at section 2187. It leaves in ten minutes, you don't have much time."

"Copy that." Anakin replied. "2187, I see it from here." Anakin increased his pacing towards the vessel. "Wait, Master. What about my Lightsaber?"

"Keep it with you at all times. It may be you're only way out if there is no other escape. Even if you get caught, it must be used as a last resort. Keep it hidden!"

"Yes, Master." When no one was looking he silently boarded the ship. Anakin took a seat towards the back as the pilot was asking for tickets from the passengers. The Besalisk tromped through with his four massive arms and body. Needless to say it wasn't long before he went to the back of the shuttle. He approached Anakin with a menacing face.

"Where to?" He asked with a booming voice.

"Mandalor," Anakin said discreetly.

"You got a ticket?"

Anakin outstretched his fingers and made a waving gesture towards the Besalisk. "You don't need my ticket."

"I don't need your ticket," the creature repeated with a slight growl. He turned around towards the head of the shuttle and left Anakin alone.

When the pilot disappeared in the cockpit, Anakin silently sighed with relief and slouched in his seat. He kept his distance from the other passengers and talked to no one. He could sense their skepticism that he was a Jedi. He avoided conversation with any one. He did anything he could, which was nothing at the moment, to keep his cover. He kept his lightsaber hidden under his cloak.

Anakin was never find of the planet or its citizens. Yes, they had close and peaceful relations with the Republic and Separatists in one hemisphere, but the other side was nothing but civil war and violence.

The shuttle slightly shook before going airborne. It shifted direction and exited the atmosphere of Corusant. Anakin could hear the rear engines activating and whirring. Out in space, the stars and distant galaxies blazed past the ship and in less than three seconds, they were in hyperspace.

 **Author's Note:**

 **Hi guys! I hope you enjoyed the first official chapter in this re-write of the prequel trilogy of Star Wars. I mean, come on, they NEED to be re-written. Did you like the fact of Anakin as a little kid was only a prologue and not a 2 ½ hour movie? For all of my hardcore Star Wars fans, you may or may not have noticed some "subtle" references to Star Wars canon. The references may be acknowledging the Original Trilogy, the Prequel Trilogy, Star Wars: The Clone Wars animated series, or Star Wars: Rebels animated series. If your confused about any events that happen or need clarification, let me know and I'll try to answer as soon as I can. If you catch any references to anything in the canon (people, places, events, etc.) tell me in the reviews. If you see something in this re-write that you like that should have been in the prequels say something in the reviews, I really enjoy the support!**


	3. Infiltration

Anakin felt his body jolt forward when the ship exited hyperspace. With no words he silently disembarked the vessel and onto the docking bay.

"The number of the cargo ship is 577. Section 410," said Obi-Wan. With too many people, Anakin didn't respond. It wasn't long until he found the cargo ship. He boarded it and eyed the trainee co-pilot in the cockpit. She glanced at him and gave a subtle nod to signify she knew who he was. She wasn't much older than him, maybe only two or three years older. But no one could tell that just based on looks of course, they he almost seemed to be the same age as her. She had long blonde hair with a brown highlights. Portions of her hair were braided, but all of it was in a tight bun fixed perfectly on top of her head. And her purple uniform made her seem official.

"Be safe," she said so softly it was almost a whisper. "The cargo may be unstable." She winked at him.

Anakin was confused. He didn't understand what she meant or why she winked, but he just shook it off.

He looked around for a place to sit. He pushed down a seating platform when something caught his attention out of the corner of his eye. It was a sign. A caution sign. Anakin translated it and comprehended the phrase. 'Warning. Cargo may be unstable. Use caution in the cargo hold.' An arrow below the words pointed towards a door in the back of the ship. Anakin was intrigued. Obi-Wan said something about his disguise being hidden on the ship. Perhaps the woman spy was hinting where to find it?

"Oh! Senator Qal! I didn't expect to see you here," the spy said unusually loud. She shot Anakin a glare which he took as his cue to hide. Fast. After all, Senator Qal of Corellia was a powerful Separatist leader. Luckily, he was successfully out of sight in the cargo hold mere moments before he came on board.

"What are you talking about? I've been commissioned to supervise the transport of the merchandise. Kaminoans always prefer one on one negotiations." He replied with a deep voice.

The sounds were blocked through the thick doors. Anakin observed his surroundings. In a compartment in the wall contained a neatly folded red and black separatist uniform. _This must be my disguise,_ he thought. He felt a rumble come out from under his feet. A sudden shift in acceleration threw him backwards off his feet. Once again, he was in hyperspace. Anakin put on the outfit, and put his usual Jedi robes in the compartment where his disguise/uniform was. He cleverly hid his lightsaber holster under his belt so the actual saber stayed secure in his pocket. He placed the data chip in the other pocket to create a similar unevenness that closely resembled his other pocket.

When the ship finally landed, the spy on board waited until the coast was clear before going to talk to Anakin. She pressed a glowing red button that turned green when she pushed it. She saw Anakin holding tightly onto a railing.

"The coast in clear, Officer. We depart back to Mandalor in four hours. I'm on the same channel." She tapped her ear three times with for index finger, signifying she had the same earpiece Anakin has. "When you are on your way back, tell me. The code term is 'Joen'."

"Got it," he replied.

Anakin got off the ship and saw Senator Qal turn a corner and disappear behind a wall. It was a bright day on the watery planet. From the platform Anakin was standing on, he had two ways to go. Left to a transparent tunnel that went underwater, or right to a smooth white building where Qal along with two Kaminoans went. He went left.

As he came to the bottom of the tunnel, he couldn't believe his eyes. A complete generation room with thousands of large glass-like cylinders with translucent green liquid. Each one containing the same naked, vile looking creature. This was the Clone base all right. The central computer had to be close by. Aha!

Smack in the center of the room. Right below the DNA chamber. Was, to Anakin's dismay, a secondary computer. It didn't have all of the information, but perhaps something within may be useful. Anakin installed the data chip and placed ten seconds in it. Ten seconds passed. He removed the chip and placed it back in his pocket. He exited the regeneration room into the next corridor.

The bright white lights coming from the floor were almost blinding. But most of it was absorbed by the dark water outside of the tunnel. Nonetheless, Anakin kept walking into the next corridor

"Comrade!" came an unforgiving voice from the side of him. Anakin snapped his head to face him. "What the hell are you doing?! We are to report to the central docking bay in five minutes!"

 _I'm getting sick of these stupid docking bays._ Anakin thought.

"Round up your squadron! Now! _He_ will not be as merciful as I am!" The man gave him a menacing stare before turning to another hallway. Anakin could hear the fear in his voice in the middle sentence.

 _He? Who is_ He _? If this guy is afraid of him, perhaps he knows the leader._

"Ana...zzzzzzzz...don't...zzzzzzzz...you nee-...zzzzzzzz...Anakin!...zzzzzzzz"

"Master, I can't understand you. Master? Obi-Wan!" The loud static buzzing filled his ears. Something was clearly blocking his communication frequency. Anakin didn't think this was unintentional.

With obviously no troopers to rally, Anakin just continued walking down another hallway. He stopped. He felt a sudden shiver slowly crawl down his spinal cord, a massive weight as is someone dropped it on him, and a whisk of freezing cold air across his body. He tightly clenched his fists and released them when the experience was over after a brief moment. He sensed a disturbance in the force. How was Kamino being influenced by the dark side? Why didn't he feel this before?

Anakin used his instincts to local the source of the dark side surge, and in less than three minutes he found himself at yet another docking bay.

Anakin assumed his position in between large, perfectly placed trays of the troopers. Without a second to spare a ramp from the cruiser came landed on the platform and a cloaked figure walked between the perfect arrays of troops, captains, and admirals, with escorts behind the person. Anakin took a good look at one of the escorts. A small object that seemed to be a bolt of some kind was stuck on the shoulder guard of the armor. This accessory wasn't seen on any of the other troopers, and he became suspicious.

"At ease," said the cloaked figure with a shrill, haunting voice. "You all are wondering why you have been summoned here. Six hours ago, our victory over Geonosis also left us with a little souvenir... A tracking beacon on one of the units," He was referring to the clones. The figure raised his voice. "Which means one of you is a bloody spy!" The figure outstretched a red and black hand and caught the clone he dragged towards him with the Force by the neck. "And as soon as I find the traitor among us," He looked at the clone in his eyes straight through his helmet, squeezing his neck tighter and tighter as he spoke. The clone attempting to become free of his grasp and gasping for air until he was no longer moving, breathing, or alive. "They will have a fate worse than death." He dropped the clone's lifeless body on the floor. The armor molded to where the killer's fingers were. "Do I make myself clear?" He snarled at the other officers and clones. They looked into his yellow eyes with fear. Glowing, yellow eyes that were full of rage and mercilessness. No one spoke. Anakin couldn't believe what he had just witnessed. The ruthless leader of the army removed his hood as he faced them. "I will find who is responsible for exposing our base," His evil red and black horned face only frightening them more. "And any accomplices are certain to suffer the same fate," he said through bared teeth before stepping over the soldier he had just murdered.

As the army dispersed, Anakin's eyes crawled back to the trooper that he saw with the 'accessory' he saw before. _I may be a spy, but I'm no traitor_ Anakin thought.

He followed the clone silently. Down several dark corridors and passageways. Finally, they hit a dead end.

"Hey!" Anakin shouted. The clone's attention was caught.

"Yes, Admiral?" the clone replied.

With ease, Anakin removed the tracking beacon from the armor of the clone and crushed it in his hand. He chuckled slightly. "So it wasn't luck that the Republic found this base, it was stupidity." Next thing he knew, the clone hit him in the temple with the butt of his laser carbine, then he bolted. Anakin ran after him. The clone began shooting him, Anakin didn't attempt to grab his lightsaber. He dodged and hurdled every blaster bolt the clone shot at him. However, it didn't stay that way. he was following the sight pattern of the clone's shooting tactics. Unfortunately, the clone caught on. While the clone was looking at his chest, his true goal was to shoot Anakin in the foot. Which is exactly what happened. Anakin fell to the ground unable to walk or break his cover. Now Anakin was groaning and struggling to get up. His foot causing excruciating pain, and his bloody nose wasn't helping either. The trooper grabbed Anakin by the collar and threw him against the wall of the tunnel. Anakin saw him raise his gun and swing his arms. Then black.

 **Did you catch the references? Who is the leader of the clone army? Review it!**


	4. Escape

Anakin regained consciousness. But he only to find himself wheezing and at gunpoint from the clone that had just knocked him out. He slowly stood up on his foot, but the laser carbine stayed targeted on the bridge of his nose. He observed his surroundings. They were in what seemed to be a repair room for droids. He couldn't see their eyes through the dark lenses of the helmet, but there was something different about this unit.

"You're not a clone."

The person behind the armor put the gun back in its holster, then proceeded to whack Anakin on his bruised nose with an armored fist. " _If_ I wasn't, you have no proof of such a conclusion." said a monotone voice of a clone through the helmet.

"Then why did you spare my life?" Anakin knew this 'clone' couldn't answer this. No response was given. "A true official among _this_ army would show no mercy. If you were a _true_ clone you would have killed me on the spot to keep word from spreading it was you that exposed this base." Something else came to Anakin's mind. "You're a spy, aren't you?"

In return, he received a punch to his right cheek. "If I was, how would I know you wouldn't turn me in and watch _him_ give me the death any traitor deserves?"

"Ah, that's the thing," Anakin paused to take a deep breath. "You're not a traitor. You wear the armor of a clone, but you sure as hell don't act like one. If you were defective, you would have been dead a long time ago. I know you're a spy."

The person in the armor hesitated to say anything. Instead, they fixed the gun towards Anakin again.

''Relax," Anakin revealed the data chip to the spy. "I'm a Republic spy, too." He groaned as his temple throbbed and he put the chip back. "How long was I out?"

The disguised person lowered their defenses and removed their helmet. It was a woman, exactly the same age as him. She had pale skin and short, messy brown hair that barely touched her shoulders. Her piercing lavender eyes were a dead giveaway that she was from Naboo. Her stern expression told him she didn't trust him completely. Anakin may have figured out she was a spy, but she still kept her true identity from him. "Two hours. Why are you here?" she asked, finally talking in her normal, unaltered voice.

"I was sent to acquire information," Anakin paused to take a deep breath. "Anything that might reveal a weakness."

"Where are you reporting this to?" she asked cautiously.

"Corusant." She had to believe him now. Corusant was the capital planet of the Republic senate.

"I was ordered to get information, too," she confessed. "Instead of weaknesses , my purpose is a map and the coordinates of the base. The beacon you destroyed doubled as an extractor for digital information, so we'll have to use yours." She said as she put her helmet back on. "If we can find a primary computer somewhere in this place, we should be able to find what we both want," she said in her modulated clone voice. "Can you walk?"

"I don't know, if we need to make dash out of here, I think I could manage."

"Fine, hold on." She grabbed Anakin by the arm and supported his weight on her shoulders. He put his weight on her. She stood up with all of her strength to support him. Both of them know made their way out of the hidden control room and into the main corridors.

"Wouldn't a computer be in the room we were just in?" Anakin whispered.

She scoffed. "Those computers are useless. All they contain are some blueprints and inventory for droid parts. Nothing we need. Besides, there are at least thirty of those labs in here."

The pair made their way down the hall a little ways when another unforgiving voice came behind them.

"Comrade! Trooper! Where are you going?" This person seemed less harsh and slightly more approachable than the last man Anakin encountered. She wore a red and black uniform identical to Anakin's except for the numerous badges showing her rank and accomplishments that were sorely lacking on Anakin's.

"Uh, to find a medical droid. I encountered the traitor. They attempted to shoot me and knocked me unconscious. Hadn't this soldier found me, things could have been much worse," lied Anakin.

The woman seemed interested. "Really? Did you catch the unit's designation?"

Anakin briefly stuttered. "N-No. But the clone was a third class air gunner." He was breathing silently and rapidly.

"Great work, Comrade. You go on and patch yourself up in sickbay, I will report this to Maul." Her long ponytail whisked around her shoulders as she turned around and walked off.

"Third class air gunner? How did you know that would work?" the spy asked in her modulated voice.

"You'd be surprised how much you take in during a time of war. The several years of training help a lot, too." said Anakin.

"Yeah, tell me about it."

They took several turns to a hallway with many doors. They were all identical. Anakin knew none of these were the the main control center, but he still played dumb. "Where are we going?"

"Somewhere heavily guarded."

After about ten more minutes of walking, they came upon a dead end. There no guards, and all that was there was a large black door with a complex keypad next to it. She picked up Anakin's hand and removed it from her shoulder. She walked over to the keypad while simultaneously removing some tools from the utility belt that hung around her waist. She took out a smaller hand blaster from another holster. "Catch."

Anakin was caught a little off guard by this and almost dropped the blaster, but managed to catch it moments before it clattered to the floor. "Watch my back, will ya?" she said.

Not long after Anakin turned around, there were several clicks and then a satisfying beeping noise. The security was successfully bypassed. The door opened with a soft whirring and they entered the control room. The door closed behind them when they entered. The room was smaller than Anakin envisioned, but the main computer stuck out like a sore thumb. A large entanglement of wires seemed to go in every direction from the device. Both searched for an outlet that the chip could fit into, but neither of them were having the best luck. The spy took off her helmet. Anakin put his gun in the pocket in place of the chip.

"Hey, who that person that woman was referring to? Um, Maul? Who's that?" asked Anakin.

"You saw what he did to that clone. That clone was innocent. It disgusts me to someone die at another's expense."

"How exactly did you evade that? I mean, you were posing as one of the escorts, wouldn't that have been the most vulnerable position to get caught?"

"That clone was an escort, too." She paused to take a deep breath as if she was on the brink of crying. "Once I new Maul saw the beacon on him, I took it off and put it on myself in hopes the Republic would track the signal. Clearly they did. I mean, you're here, so..."

"Yeah, I got it." Anakin said. "Any luck with the outlets?"

"No. Not on any of the secondary computers here either."

Something was wrong. About this base, about it being influenced by the dark side, how there was absolutely no protection for the main computer.

"Wait, I thought you said this place would be heavily guarded?" Anakin said.

A blaring sound echoed through the room. The spy came to a realization. "Oh, crap!" but it was too late. The large door opened revealing a large squad of clone troopers with their defenses raised. The clone who stood out the most bore a thick blue stripe painted down the armor for his arms and a blue shoulder ornament with one blaster in each hand. He shot the chip out of Anakin's right hand rendering it useless as it clattered to the floor. Anakin shot the internal control panel with his handgun and the doors closed, separating them for the time being.

"Great work, genius. How are we supposed to get out of here, now?" The spy snapped. "Both of our missions are failures."

"Not completely. I think I can still extract the data."

"How? Even if we do get the information, how are we supposed to get passed them?" she asked.

Anakin took notice of a door on the opposite end of the room from the door. Inside was a string of surveillance equipment of the base being controlled by a tactical droid. It kept repeating "Door lock malfunction, resetting program; door lock malfunction, resetting program".

Both of them had the same idea. He pinned down the droid where he was sitting, and she ripped off the headpiece. As this was done, the head gave of a small amount of sparks and the droid made a sound as if it was shutting off. With help from her armor, she broke one of the arms in two to give a sharp edge to cut through the head. Anakin rummaged through the wires and the motherboard until he found and removed the hard drive. With success, it fit into one of the outlets in the previous room and managed a partial data upload. Anakin replaced the handgun with the hard drive in his pocket. "I'll try to get the door open, you try to shut this alarm off!" He yelled over the deafening noise.

When the spy turned around to attempt to shut off the noise Anakin outstretched his hands and ripped the door out of its frame with the Force, killing all of the clones that it hit before crashing into a wall just as the alarm finally stopped.

They silently exited the room, but both stayed vigilant. Another blockade of soldiers could be lurking behind anywhere and attack at any moment. Any means of escape was uncertain at this point. Their goal was to make it back safely into Republic space. They had what they came for, now a new question loomed above both of their heads: What now?

 **Who is the spy? Will they get out alive? Did you catch te references? Review your thoughts and find out in the next chapter!**


	5. Safety

**Hey, guys! Sorry it's been a while. Stuff got in the way. I hope you like the chapter!**

The underwater facility was like a maze. Anakin was forced to rely on the spy beyond the droid repair room from which they decided to work as a team and blindly trust each other. She seemed to know her way around the base, but it seemed to be going nowhere. Anakin heard an annoying buzzing from his earpiece.

"Anakin...zzzzzzzz...Come i-...zzzzzzzz...Wha-...zzzzzzzz...Can you...zzzzzzzz..."

It seemed to be receiving a slightly clearer signal, which meant one of two things. They were getting closer to the perimeter, or they were only getting closer to the surface. Either way, at least they were making progress. A little bit anyways.

"Commander Skywalker. Senator Qal's negotiations with the Kaminoans will end soon. You need to be on board before he finishes," said Fora, the spy onboard the cargo ship. "I'm having trouble contacting Corusant, is the same thing happening to you?" she asked.

"Yeah, so far you're the only person I've had been able to actually talk to over this thing," he replied. "Can you delay the departure? I ran into some trouble down here."

"I'll do what I can, but I can't guarantee a large time window." She sounded worried. Faint gunshots came into the microphone. "Is everything OK? Why am I hearing blasters?"

Anakin paused, not knowing what to say. "Skywalker out."

Anakin went to investigate the sounds himself. He found two dead clones on the floor on their backs. The woman whom he was with held an additional laser carbine in her left hand and clutched her left elbow with her right hand. She didn't seem to be bleeding severely, but she was clearly in pain. Even if her face wouldn't show it.

"What happened?"

"Well, while you were talking to whoever you were talking to, _I_ was watching our back. Two troopers found us. I took care of them. End of story." She said impatiently, subtlety wincing.

"You can't shoot, now. They clearly hit you in the arm." Anakin said gesturing towards her injury.

"Relax, I'm fine. I can shoot with my other hand. It's not like my arm is broken. Here, take this," she handed him the gun. Anakin took it from her.

"That doesn't excuse the nerve damage." Anakin paused at the sound of uniform footsteps in the distance. "We don't have much time, we need to get out of here."

"You have a ride out of place?" She asked, still clutching her arm.

"Yeah, the closest entrance where the Kaminoans reside above water." Anakin told her. "If you take me to the docking bay where Maul came in, I know the rest of the way."

"Nope, can't. Anywhere near there will be swarming with troopers. It's too risky since they already saw us," she said. Anakin looked discouraged. "But I know another way. Keep up if you can," she smiled at him, briefly glanced at his foot and drew out her pistol.

She ran and Anakin followed with the bulky blaster in hand. Their injuries made them slower than usual, but they managed to keep out of harms way for the time being. She didn't bother to look over her shoulder. Anakin continued following her until they stopped at a hatch in the ceiling above them. Anakin pried the doors open with the Force. It took her a second to figure it out, but when she did she was speechless and looking at him surprised and slightly conflicted. After the doors were successfully opened, Anakin knelt down and locked his fingers together. She already saw hi use the Force, so there was no need to hide it from her any longer.

"Jump up, I'll be right behind you." he assured.

She stood there unsure what to do, but finally stepped onto his palms and flew up the shaft with Anakin's assistance with the Force. He looked up and saw her grip a handle with her right hand and swing down another tube out of Anakin's vision. He pushed hard against the floor (mostly on his uninjured foot) and shot up and grabbed the same handle. Before he followed her down the same path, he used the Force to fix the broken shaft doors just before an army of clones passed under it.

"Down here!" her unaltered voice echoed in the metal pipe. Anakin made eye contact and slid down to land on his feet. He found himself in a room with several sets of clone armor somewhat similar to what she had on before except with a more bulky shape, a window for the face instead of just eyes, and cylindrical tanks mounted on the back. She seemed to be having trouble attaching a wide collar to her armor and two cylindrical tanks she wore on the back of her suit were supported on her by one shoulder like a backpack. Anakin took the collar from her and attached it around her neck himself, as he did this, a mechanical sealing sound occurred. He then lifted her limp arm and slipped it through the other strap. She could barely move it, much less feel anything with.

"Thank you," she said attaching the tubes to the collar and grabbed her helmet. "You better put on a suit, too. We're at least a couple hundred feet below the surface."

Anakin took her advice and put on the pressurized armor, oxygen tanks and helmet. The armor didn't quite fit him, but it would have to do. He placed the helmet over his head followed by a sealing sound and faint robotic breathing.

"These suits should have built in comlinks, can you hear me?" she said with a slight change in her voice due to the filtering through the speakers.

"Yeah. Yeah, I hear you. Clear as day," Anakin replied.

"Good. Come on." she gestured for him to follow her.

"Wait, what?"

He followed her, but she wasn't listening. A door sealed she rotated a knob in the wall. The labeled increments of pressure next to them rapidly increasing more and more each time she did this. Both her and Anakin felt the excessive amount of weight on their shoulders, they both struggled against the pressure. "Trust me, if you weren't wearing this equipment, you'd be dead." She pushed a button on the wall but nothing happened. She pushed it again. Still nothing. She repeatedly pushed it impatiently, but with no success. "Sabotaged! We're trapped." she told Anakin.

Something clicked in his mind. "No... we're not," he said.

"What are you talking about?" she asked.

"Shatter point," he answered.

He bent down and pressed his covered palm on a weaker spot on the clear substance that made up the cube they were standing in. Within a few seconds a large series of cracks grew from the center of his palm made contact with the floor. They continued to grow until he raised his hand and stood up next to her. All that was left was a web of fractures beneath their feet. Anakin outstretched his palm and pushed the shards into the bottomless oceans of Kamino without even coming close to them. The water stayed stationary under them, it didn't move. She looked at him reluctantly, then at the water, then at him. She held out her hand and Anakin took it. They both jumped in the hole and began to swim towards the surface. They looked up at the light pouring in from the surface as they grew closer.

"Joen! Joen! We need a pick up on the surface in two!" Anakin exclaimed to Fora.

"Copy that, Commander. Fora out." Fora replied.

"Who was that?" the other woman asked.

"Our ride." Anakin said in reply.

When they reached the surface, Fora caught sight of them almost immediately. From the rear of the ship, a hidden ramp lowered partially in the water. Anakin used this to his advantage and climbed on with his new friend in tow. They both sat down as they removed their helmets, gasping and coughing at the sudden shift in pressure. She winced in pain and clutched her arm again. A large red stain blossomed from her elbow inside the suit. Anakin quickly took off the pressurized suit and found his normal Jedi robes. He found the outer cloak and ripped off the hem. He removed the heavy duty glove from her hand and pushed up the sleeve to expose her arm. The wound looked like it was burned with acid. Anakin used the fabric and proceeded to tie it around her arm as a tourniquet. "I'm not a medical droid, but that's all I can do for now."

She just sighed as she sat there. "Thank you, uh..."

"Anakin," he finished. "Anakin Skywalker."

"I'm Padmé." She said. "Padmé Lars."

Anakin went to rip another portion of his robe off for his foot. "Nice to survive with you, Padmé." He said.

"Nice to outrun a deadly clone army with you, too Master Jedi." Padmé remarked. Anakin snapped his head towards her in shock. "Don't be surprised, Anakin. I know a Force-user when I see one," she said calmly.

After Anakin bandaged his foot, he heard Obi-Wan's voice again.

"Anakin, what happened? Why aren't you responding?"

"Master! Umm...there was something blocking foreign transmissions within the base."

"Did you run into any trouble while in there?" Obi-Wan asked.

Anakin paused. "Yes. Quite a bit actually." He briefly made eye contact with Padmé "But the mission was a success." he said in an attempt to change the tone of the conversation.

"I expect a thorough debriefing of it all when you return. Great work, Anakin."

"You're welcome, Master." Anakin answered. "Skywalker out."

Anakin was caught unprepared when the ship entered hyperspace. His body was thrown to the floor next to Padmé who stared at him from her sitting position. She chuckled slightly at the scene. Anakin felt himself blush ever so slightly, but then began to laugh at himself, too. Anakin didn't have many friends outside the Jedi Order, and this friendship was off to a pretty good start considering what the previous couple of hours endured for both of them.

 **What do you think? Better start than what 'The Phantom Menace' gave us? Did you catch the references? Let me know in the reviews!**


	6. The Debriefing, Part 1

**Hey guys, I know its been quite some time since I** **updated this story, and I'm very sorry about that. But on the plus side, it's given me some time to improve some of the scenes for later in the story, and I can't wait for you guys to see it!**

Padmé and Anakin remained silent for most of the trip. They didn't exchange any conversations, they had to stay quiet since she wasn't supposed to be on the vessel in the first place, and with no cargo to transport, anything that was said would echo all throughout the cargo hold, and very likely be heard by anyone in the passengers area.

Both sat there bandaged, bruised and silent. They could ignore the pain. They've both endured much worse. After all, it was wartime.

After what felt like hours, the time finally came to get off the ship. Fora came in to tell Anakin that the coast is clear, but was suddenly alarmed when she saw Padmé and the scattered pieces of clone armor. "Who is that?" she asked.

"I had no choice, w-"

"She wasn't assigned to the mission, nor were you supposed to take prisoners," she interrupted.

"She is not a prisoner, she's a Nabooan," Anakin explained. "She's on our side."

"We're wasting time, you need to get off. Now." Fora shoved both of them out of the ship. "Now I have to clean up your mess," she said referring to the pieces of scattered armor.

They strolled around the dock for a little while looking for a way off the Mandalorian docking platform. Something Anakin said clicked in Padmé's mind.

"How did you guess I was from Naboo?" she asked.

"Huh?" he replied, snapping his focus towards her.

"That woman back on the ship. The one who assumed I was a prisoner? You told her 'She's not a prisoner, she's a Nabooan. She's on our side'," she said. "How did you guess that?"

Anakin paused for a second, lost for words. "Oh. Um, people with a purple eye color usually are from Naboo, or come from Nabooan lineage. It wasn't exactly hard to figure out."

She looked at him reluctantly.

Both ran up to the droid selling transport tickets not far from them. Anakin was about to ask when the next one for coruscant was, but Padmé beat him to the line and asked "When's the next one leaving for Naboo?" The droid told her seven hours.

"That's too long, is there anything sooner?" she asked.

"Sorry," the droid replied.

Anakin came up behind her. "What about Corusant? What time is that one coming?" he asked.

"Forty-five minutes," said the droid. Padmé grew an annoyed expression.

"Anakin I have to go to Naboo," she whispered rather loudly.

"We'll take two passes for the next shuttle to Corusant," Anakin said. The droid printed two tickets from a slot in his outer thorax shell and handed them to Anakin. He paid the droid with some credits buried deep in his cloak.

"Anakin, I have to get to Naboo," Padmé told him. "I need to go home."

"And you will. But we both have to give a debriefing to the counsel," he explained.

This was all it took to silence her. Padmé knew exactly who he was referring to. She has never stood in front of the Jedi counsel before, and she was dreading the evaluation.

* * *

The blazing Mandalorian star that heated the planet was becoming overwhelming for Padmé. The fact that she was wearing a black jumpsuit and in bare feet wasn't exactly easing the discomfort. Sweat was beginning to become absorbed by her black body suit, which was baggy in many areas. She walked towards a shady area to rest until the passenger shuttle arrived. Anakin followed closely behind to join her. She leaned against the wall and felt her back rub against the cool, shaded metal as she sled down into a sitting position. She had to move her injured arm since it just started to her more as she inadvertantly sandwiched it between her knees and her stomach. Anakin didn't sit next to her, but he briefly looked at her as she slid towards the ground. he leaned mostly on his uninjured foot while he stood. Both stayed in the shade for the duration it took for the shuttle to arrived.

Both of them boarded with ease. They showed their tickets to the stewardess droid and took their seats. No mind tricks necessary. Anakin wanted to get close to her, just on the off chance she managed to bolt away from him, but wasn't sure if he should on the account of seeming too suspicious. He kept a safe distance from her on the shuttle sitting in the seat across the aisle from where she was.

The ride to Corusant was about what Anakin expected but with one exception. The vehicle was packed with no empty seats, and the atmosphere was littered with words being exchanged between passengers, but Padmé was surprisingly silent. Although he didn't know why, Anakin could sense she was feeling uneasy, and it wasn't because they were traveling through hyperspace.

 _... Anxiety?_ Anakin thought to himself. _But why?_ She managed to slip by enemy lines undetected, and if it weren't for her, he would probably still be stuck on Kamino. Both have accomplished so much for the Republic today. Granted, both of them were injured, but it's a small price to pay considering how many people have already died from this war. _She should be proud, not nervous._ Without realising it, he was looking at her the whole time he was thinking about this. When she snapped her head towards him, Anakin quickly turned away, but there was no way he could recover by saying he wasn't looking at her.

"You're nervous," he managed to tell her through the boisterous background noise. "Why are you so anxious to get home?"

"I'm not _anxious_ ," she defended a little too quickly. "I'm expected back, and I can't keep them waiting."

Anakin wanted to believe her, but he knew there was something she wasn't telling him.

"Them?"

Padmé stayed silent. She kept a straight face, but she was slowly turning red as Anakin continued questioning her.

"Padmé, you're going to have to explain sooner or later, but you can trust me. After all, you did just that with me back there," Anakin said while being very careful with his words.

"Why should I trust you, Anakin? Why? Because you're a- ... politically powerful person?" She said saving herself just in time. If the word 'Jedi' did manage to slip out, it would have meant trouble for both of them.

"No, because- look, we can't talk about this right now. Just... stay close when we get there, alright?"

Padmé made no comment and stayed silent for the rest of the trip to Coruscant.

* * *

When the shuttle landed, Padmé didn't bother to try to run off. Although she could out run him, it wouldn't do her any good. She knew that there wasn't any way she was getting out of this. Her heart thudded harder and louder as they left the docking bay and entered the capital building. She heard Anakin put one finger to his right ear and talk to someone who wasn't there.

"We've arrived, Master." Anakin spoke, "when is the debriefing?"

" 'We'?" Obi-Wan said over the communicator. "Anakin, wh-"

"Don't worry Master, I can explain everything. When is the debriefing?"

"As soon as you arrive to to the main tower. And who is this _girl_ you brought with you?" Obi-Wan asked.

Anakin looked confused for a moment, but quickly caught the silhouette of his master standing in one of the large windows above the docking bay. He couldn't decipher his facial expression, but he had a strong feeling that is wasn't an amused one.

"I assure you master, I can explain everything," Anakin repeated. "We will be in front of the counsel in fifteen minutes."

"Very well. I'll alert them that you're coming." Obi-Wan responded.

"Thank you, Master."

Anakin and Padmé slowly made their way through the main capital building to the tallest tower within it. When they approached the door to the meeting room of the Jedi counsel, Obi-Wan was standing beside it. Anakin couldn't tell whether his master was proud or disappointed that she was with him. He could only imagine what the counsel's reaction would be.

"Anakin, before I let either of you in there, I must ask, did you acquire what you were supposed to?" Obi-Wan asked. Anakin said nothing and only gave the memory chip of the tactical droid to him. Judging by his expression, Anakin knew Obi-Wan was not expecting the memory chip of a discontinued droid model containing such sensitive information. Nonetheless, he still took the chip and put it in a hidden pocket within his robes. "The council will see you both now," Obi-Wan told them. Anakin stepped into the counsel chamber with confidence, but Padmé's heart was racing faster than ever. She should feel her palms sweating, and she knew it wasn't from the temperature of the oversized black bodysuit she wore at that time. The made their way to the center of the room, nearly blinded by the vibrant sunset. The surrounding orange and silver throne-like seats were all occupied by high council members. Not one hologram was in place of anybody.

"Would you consider your mission a success, Skywalker?" said the slightly muffled but shrill voice of Plo Koon.

"I- excuse me, Masters. _We_ acquired as much information as we could about our enemy, including their battle tactics and some bases and allies. I was hoping to gather knowledge of who the host for their clone army is, but I wasn't able to escape without any intel of who they might be or even some DNA. Aside from that, we both succeeded in hacking into the central computer for the base and picked up as much data as the chip would carry. It's a small sliver of the power of the overall information stored into the computer, but it should provide at least a small handful of opportunities that would turn the war in favor of the republic."

The counsel remained silent for a few moments as they contemplated what Anakin had just said.

"And you, Nabooan?" a calming female voice said. It was Luminara Unduli. Her shearing ocean-blue eyes staring directly into Padmé's. "How did your mission intersect with Skywalker's?"

Padmé was placed a little on the spot when she was asked this. "Uh, w-well you see, Anakin saw the tracking device on the armor that I was wearing while I was undercover in the base. He was disguised as an officer for the enemy, so I thought he had caught on to my act. Out of impulse I ran. As I ran, I also started... shooting... at him with a laser carbine I stole from the same clone I stole the armor from. I only hit Anakin in the foot, but since he couldn't walk at that time, I took advantage of the opportunity I had and rendered him unconscious. I dragged him to a droid repair room hoping to keep him silent because I thought he was an enemy." She knew if a Republic citizen committed foul play against a Jedi, whether a Youngling, Padawan, or Master, it was a crime eligible for the death penalty. She was hoping she wouldn't have to bring it up, but if she didn't, she could be charged with perjury. " But somehow, Anakin saw through my act and we both realized we were on the same side. We decided to help each other complete our missions because neither of us could complete our missions without something the other had." Padmé finished.

"Skywalker, Is what she just said true?" Luminary asked him.

"Yes, Master Unduli, every word." Anakin confirmed.

Hardly a moment of silence passed through the chamber when a deep voice spoke, "Thank you, Anakin, that'll be all for now. You will be called back for further questioning momentarily. Miss Lars will stay for now." Mace Windu's voice never failed to leave anybody nervous.

Padmé shot a quick glance at Anakin as he was making his leave. He caught her terrified gaze and mouthed 'You're doing great' to her. When the humming of the closing doors stopped, Padmé brought her attention back to the debriefing. She made eye contact with Windu and immediately put down all of the fear she was housing in her chest, for it had been replaced with slight anger and immense confusion. "How did you know my name was-"

"You aren't as subtle as you think you are when it comes to espionage, Miss Lars," Mace told her. "That isn't your real name is it?"

"No," she was clenching her fist. She wanted all of this to be over with. What did they want from her?

"Well what is it? Your face isn't recognized in any of the criminal records, nor a member of the Separatists or the enemy. Tell us, what is your name?" Mace repeated himself.

Clearly, she wasn't going to fool anybody in the room. Nor could she think of a safer place to reveal herself, either. She dropped the sassy persona she created for herself and puffed her chest. "I am Padmé Naberrie Amidala," she told them. "I'm sure you all have heard of that name, and I will agree to continue with this debriefing in exchange that I see the information extracted from the prior mission. It only seems to be fair." No one on the council seemed to disagree with these terms and so the debriefing resumed.

"Under who's authority were you sent on the mission?" Shaak Ti asked her.

"My own, Master Jedi. I would rather die on the mission for my people than risk any one of my warriors, the mission was far too risky and important, and I had been trained in combat from a young age."

"How were you able to get into the base?"

"During the battle of Geonosis, I incapacitated one of the clones. I stole his armor and weapons and snuck onto the enemy ship when they were retreating. I enabled the signal after the ship departed in hopes of the Republic finding it," Padmé answered. She was feeling much more confident now. She stood still and silent waiting for another question to be given to her, but no one spoke. Finally a raspy voice broke the silence.

"For your time, we thank you," Master Yoda said. "Show you the chip, we shall, after Skywalker is questioned."

"Before I leave there is one more request I have," Padmé started. "I wish for the word of my true identity to remain in this room. Please let anyone who knows me as Padmé Lars still know me by that name. I know it's dishonest, but it's for the best."

Yoda stroked his chin in deep thought for a few seconds. "Hmm. Very well. Safe, your secret is with us, Your Highness."


End file.
